vmd-tutorial.Bioinfo.2009

Description

University of Illinois at Urbana-ChampaignBeckman Institute for Advanced Science and TechnologyTheoretical and Computational Biophysics GroupVMD Molecular GraphicsJordi CohenVMD Developer: John StoneMarcos SotomayorElizabeth VillaMay 2003.A web version, in color, is available athttp://www.ks.uiuc.edu/Training/SumSchool03/Tutorials/vmdCONTENTS 2Contents1 Basics of VMD 41.1 Loading a Molecule . . . . . . . . . . . . . . . . . . . . . . . . . . 41.2 Displaying the Protein . . . . . . . . . . . . . . . . . . . . . . . . 51.3 Exploring Di!erent Drawing Styles . . . . . . . . . . . . . . . . . 61.4 Di!erent Coloring Methods . . . . . . . . . . . . . . . 81.5 Exploring Di!erent Selections . . . . . . . . . . . . . . . . . . . . 81.6 Multiple Representations. . . . . . . . . . . . . . . . . . . . . . . 101.7 Sequence Extension. . . . . . . . . . . . . . . . . . . . . . . . . . 111.8 Saving your Work . . . . . . . . . . . . . . . . . . . . . . . . . . 122 Multiple Molecules and Scripting 142.1 Loading Multiple Molecules . . . . . . . . . . . . . . . . . . . . . 142.2 Using the Main Window . . . . . . . . . . . . . . . . . . . . . . . 152.3 Tcl Scripting Basics and TkCon. . . . . . . . . . . . . . . . . . . 162.4 The atomselect Command . . . . . . . . . . . . . . . . . . . . . 172.5 Aligning Two Molecules . . . . . . . . . . . . . . . . . . . . . . . 202.6 Using Color to Display the Deviation . . . . . . . . . . . . . . . . 223 Trajectories, Macros and ...

Informations

• Publié par: Nasheg
• Nombre de lectures: 45
• Langue: English

Extrait

University of Illinois at Urbana-Champaign Beckman Institute for Advanced Science and Technology Theoretical and Computational Biophysics Group

VMD Molecular Graphics

VMD Developer: John Stone

Jordi Cohen Marcos Sotomayor Elizabeth Villa May 2003.

A web version, in color, is available at http://www.ks.uiuc.edu/Training/SumSchool03/Tutorials/vmd

CONTENTS

Contents 1 Basics of VMD 1.1 Loading a Molecule . . . . . . . . . . . . . . . . . . . . . . . . . . 1.2 Displaying the Protein . . . . . . . . . . . . . . . . . . . . . . . . 1.3 Exploring Di!erent Drawing Styles . . . . . . . . . . . . . . . . . 1.4 Exploring Di!erent Coloring Methods . . . . . . . . . . . . . . . 1.5 Exploring Di!. . . . . . . . . . . . . . . . . . . . erent Selections 1.6 Multiple Representations . . . . . . . . . . . . . . . . . . . . . . . 1.7 Sequence Extension . . . . . . . . . . . . . . . . . . . . . . . . . . 1.8 Saving your Work . . . . . . . . . . . . . . . . . . . . . . . . . . 2 Multiple Molecules and Scripting 2.1 Loading Multiple Molecules . . . . . . . . . . . . . . . . . . . . . 2.2 Using the Main Window . . . . . . . . . . . . . . . . . . . . . . . 2.3 Tcl Scripting Basics and TkCon . . . . . . . . . . . . . . . . . . . 2.4 TheesmotceltaCommand . . . . . . . . . . . . . . . . . . . . . 2.5 Aligning Two Molecules . . . . . . . . . . . . . . . . . . . . . . . 2.6 Using Color to Display the Deviation . . . . . . . . . . . . . . . . 3 Trajectories, Macros and Labels 3.1 Loading trajectories . . . . . . . . . . . . . . . . . . . . . . . . . 3.2 Macros . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3.3 Main Menu Animation Tools . . . . . . . . . . . . . . . . . . . . 3.4 Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3.5 An Example Tcl Script: Calculating the RMSD of a trajectory .

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CONTENTS

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Introduction This tutorial introduces new users to VMD and its capabilities. It can also be used as a refresher course for the occasional VMD user wishing to employ this program more productively.This tutorial has been designed specifically for VMD 1.8.1 and should take about 3 hours to complete in its entirety. The tutorial is subdivided into three separate units of increasing complexity. The first unit covers the basics of molecular graphics representations and will introduce everything you need to know to generate nice graphics. The other two units are targeted towards the scientifically-oriented user and focus on scripting in VMD. While scripting may be skipped by the non-technical users, we encour- age everyone to give it a try as it provides some very powerful (and easy to use) tools that cannot be o!ered by a simple graphical user interface. The examples in the tutorial will focus on the study of ubiquitin – a small protein with interesting properties. Throughout the text, some material will be presented in separate “boxes”. These boxes include complementary information to the tutorial, such as information about the biological role of ubiquitin, and tips or shortcuts for using VMD.

Ubiquitin.This tutorial will focus on the visualization ofubiquitin with VMD. Ubiquitin is a small protein of 76 amino acids, that is believed to be present in all eukaryotic cells. It is one of the most conserved of all eukaryotic proteins (the first 74 amino acids form a structure that is identical in insects, trout, bovines and human) and it has been identified in the nucleus, cytoplasm and on the cell- surface. It’s primary role is in protein degradation, where it acts as a tag for intracellular proteolysis. Getting Started You can find the ubiquitin files in thefilesdirectory that came with this tutorial. This tutorial assumes that VMD has been correctly installed on the user’s com- puter. For installation instructions, please refer to the VMD Installation Guide. To start VMD, typevmdat a UNIX command-line, or double-click on the VMD application icon.

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1 Basics of VMD In this unit you will build a nice image of ubiquitin while becoming accustomed to basic VMD commands. In addition, you will learn how to look for interesting structural properties of proteins using VMD. 1.1 Loading a Molecule Our first step is to load our molecule. A pdb file,1UBQ.pdb, that contains the atom coordinates of ubiquitin is provided with the tutorial.

1Choose theFile!New Molecule... menu item Fig 1(a) in the VMD Main window. Another window, the Molecule File Browser (b), will appear in your screen. 2Use theBrowse...(c) button to find the file1UBQ.pdbin the ap- propriate directory. Note that when you select the file, you will be back in the Molecule File Browser window. In order to actu-  Figure 1: Loading a Molecule. ally load the file you have to press Load not forget to do this!(d). Do Now, ubiquitin is shown in your screen in the OpenGL Display window. You may close the Molecule File Browser window at any time.

Webpdb.VMD can download a pdb file from the Protein Data Bank if a network connection is available. Just type the four letter code of the protein in the File Name text entry of the Molecule File Browser window and press the Load button. VMD will download it automatically.

Coordinates file.The file1UBQ.pdbcorresponds to the X-ray struc- tureofubiquitinrefinedat1.8A ˚ resolutionprovidedbySenadhi Vijay-Kumar, Charles E. Bugg and William J. Cook, J. Mol. Biol. (1987)194 Note, 531. that the protein is sorrounded by 58 water molecules, and that hydrogen atoms are not included.

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1.2 Displaying the Protein In order to see the 3D structure of our protein we will use the mouse and its multiple modes.

1While holding the left button pressed over the protein in the OpenGL Display, move the mouse and explore what happens. This is the rotation mode of the mouse and allows you to rotate the molecule around an axis parallel to the screen Fig. 2(a).

Figure 2: Rotation modes.

2If you press the second button and repeat the previous step, the rotation will be done around an axis perpendicular to your screen (b) (For Mac users, the second button is equivalent to press the command key while holding the mouse button pressed).

3In the VMD Main window, look at theMousemenu (Fig 3). Here, you will be able to switch the mouse mode fromRotationto TranslationorScalemodes. 4TheTranslationmode will allow you to move the molecule around the screen while holding the first button pressed.  Figure 3: Mouse modes.

5TheScalezoom in or out by moving the mousemode will allow you to horizontally while holding the first button pressed. It should be noted that the previous actions performed with the mouse do not change the actual coordinates of the molecule atoms. Mouse modes.Note that each mouse mode has its own charac- teristic cursor and its own shortcut key (r: Rotate,t: Translate,s: Scale) that could be used instead of the Mouse menu. (Be sure to have the OpengGL Display window active when using the shortcuts.) Additional information can be found in the VMD user’s guide.

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Another useful option is theMouse!Centermenu item. It allows you to specify the point around which rotations are done.

6Select theCentermenu item and pick one atom at one of the ends of the protein. (The cursor should display a cross.) 7Now, pressr, rotate the molecule with the mouse and see how your molecule moves around the point you have selected. 1.3 Exploring Di!erent Drawing Styles VMD can display your molecule using a wide variety of drawing styles. Here, we will explore those that can help you to identify di!erent structures in the protein. 1Choose theGraphics!Represen- tations... window Amenu item. called Graphical Representations will appear and you will see in yel- low Fig 4(a) the current graphi- cal representation used to display your molecule. 2In theDraw Styletab (b) we can change the style (d) and color (c) of the representation. In this sec- tion we will focus in the drawing style (the default isLines). 3Each drawing style has its own parameters. For instance, change theThicknessof the lines by using the controls on the right bottom part (e) of the Graphical Repre- sentation window. 4Now, choose fromDrawing Method theVDW(van der Waals) menu item. Each atom is now repre- sentedbyasphe e re e . asi I ly n t t h h e is vo w l ay - Figure4:GraphicalRepresentations you can see mor u  window. metric distribution of the protein.

5In order to see the arrangements of atoms in the interior of the protein, use the new controls on the right bottom part of the window (e) to change the

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Sphere Radius theto 0.5 andSphere Resolutionto 13. Be aware that the higher the resolution you choose, the slower the display of your molecule will be. 6Note that in the Name coloring method, each atom has its own color, i.e: O is red, N is blue, C is cyan and S is yellow. 7Press theDefaultbutton. This allows you to return to the default prop- erties of the drawing method. More representations.Other interesting representations are CPK and Licorice. In the first one, like in old chemistry ball & stick kits, each atom is represented by a sphere and each bond is repre- sented by a cylinder. (Radius and resolution of both the sphere and the cylinder can be modified independently.) The Licorice drawing method (widely used) also represents each atom as a sphere and each bond as a cylinder, but the sphere radius cannot be modified independently. The previous representations allows you to see the micromolecular details of your protein. However, more general structural properties can be seen by using more abstract drawing methods.

8Choose theTubestyle under Drawing Method and observe the backbone of your protein. Set theRadiusat 0.8. 9By looking at your protein in the tube mode, can you distinguish how many helices,!sheets and coils are present in the protein? The last drawing method we will explore here is calledCartoon. It gives a simplified representation of a protein based in its secondary structure. Helices are drawn as cylinders,!sheets as solid ribbons and all other structures as a tube. This is probably the most popular drawing method to view the overall architecture of a protein.

10Choose theCartoonstyle and set theBeta Sheet Thicknessas 3, theHe- lix/Coil Radiusas 1.5. 11betasheets and coils are present in theIdentify now how many helices, protein.

Structure of ubiquitin.Ubiquitin has three and one half turns of !-helix (residues 23 to 34, three of them hydrophobic), one short piece of3 10 -helix (residues 56 to 59) and a mixed"sheet with five strands (residues 1 to 7, 10 to 17, 40 to 45, 48 to 50, and 64 to 72) and seven reverse turns. VMD calculates the secondary structure using STRIDE, which uses an heuristic algorithm that in this case shows only four of the five"strands.

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Figure 5: Licorice, Tube and Cartoon representations of Ubiquitin

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1.4 Exploring Di!erent Coloring Methods 1Now, let’s modify the colors of our representation. Choose theResTypecol- oring method Fig. 4(c). This allows you to distinguish non-polar residues (white), basic residues (blue), acidic residues (red) and polar residues (green). 2Select now theStructurecoloring method (c) and confirm that the cartoon representation displays colors consistent with secondary structure. 1.5 Exploring Di!erent Selections Let’s look at di!erent independent (and interesting) parts of our molecule.

1In theSelected Atomstext entry Fig. 4(f) of the Graphical Representations window delete the wordall, typehelixand press theApplybutton or hit the Enter key. (Do this every time you type something.) VMD will show just the helices present in our molecule. 2In the Graphical Representations window choose theSelectionstab Fig. 6(a). In sectionSinglewords(b) you will find a list of possible selections you can type. For instance, try to display!sheets instead of helices by typing the appropriate word in theSelected Atomstext entry. Combinations of boolean operators can also be used when writing a selection.

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3In order to see all that is not helix and not!sheet, type the following (not helix)and(not betasheet) 4In the sectionKeyword(c) of theSelectionstab (a) you can see properties that can be used to select parts of a protein with their possible values. Look at possible values of theKeyword resname all the Lysines(d). Display and Glycines presents in the protein by typing(resname LYS)or(resname GLY)fundamental role in the configuration of polyubiquitin. Lysines play a chains.

5Now, change the current represen- tation toCPKstyle and the col- oring method toResIDby using the previous described buttons in theDraw Style the screentab. In you will be able to see the di!erent Lysines and Glysines. How many of each one can you see? 6In theSelected Atomstext entry typewater the coloring. Choose methodName. You should see the 58 water molecules (in fact only the oxygens) present in our sys- tem. 7In order to see wich water molecules are closer to the pro- tein you can use the command within. Typewater and within 3 of protein. This selects all the water molecules that are within a distance of 3 angstroms the rotein.  Figur esentations ofp windo e w 6 a : nd G th ra e p S h e i l c e a c l tio R n e sba r t p .

8Finally, try the following selections:

Selection Action proteinShows the Protein resid 1The first residues (resid 1 76)and(not water)The first and last residues (resid 23 to 34)and(protein)The"helix

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All the previous options provide you with a powerful tool to explore di!erent parts of your protein or molecule.

1.6 Multiple Representations

The buttonCreate RepFig 7(a) in the Graphical Representations window allows you to create multiple represen- tations and therefore have a mixture of di!erent selections with di!erent styles and colors, all displayed at the same time.

1Be sure that the current represen- tation is inCPKstyle and coloring methodName 2Set the current selection as protein. 3Press theCreate Repbutton (a). Now, using the menu items of theDraw Styletab and theSe- lected Atomstext entry, modify the new representation in order to getRibbonsas the drawing method,Structureas the coloring F ur s m el e e t c h t o io d n , . andhelix giM:7e stacuheenrrt n. snfotaoi iuitbUqi pleRultisentepre

4previous procedure, create the following three new repre-Repeating the sentations: Drawing Style Coloring Method Selection Cartoon Structurebetasheet Cartoon Molecule(not helix)and(not betasheet) CPK Name(resid 1 76) and (protein)

5final representation by pressing again theCreate a Create Repbutton. Select theCartoondrawing method, theMoleculecoloring method and

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typehelixin theSelected Atomsentry. For this last representation choose in theMaterialsection (c) theTransparentmenu item. 6Note that with the mouse you can select the di!erent representations you have created and modify each one independently. Also, you can switch each one on/o!by double clicking on it or delete each one by using the Delete Rep the end of this section, the Graphical Repre-button (b). At sentations window should look like Fig. 7. 1.7 Sequence Extension When dealing with a protein for the first time, it is very useful to find and dis- play di! sequence extension allows you to pick Theerent amino acids quickly. and display one or more residues easily.

1Choose theExtensions!Sequence menu item. A window Fig. 8(a) with a list of the amino acids (e) and their properties (b)&(c) will appear in your screen. 2With the mouse, click over di!er- ent residues (e) in the list and see how they are highlighted. In ad- dition, the highlighted residue will appear in your OpenGL Display window in yellow and bond draw- ing style, so you can visualize it easily. 3Using theZoomcontrols (f) you can display the entire list of residues in the window. This is es- pecially useful for larger proteins 4Using the shift key while pressing the mouse button allows you to pick multiple residues at the same time. Look at residues 48, 63, 11 and 29 (e). Figure 8: Sequence window.

5Look at the Graphical Representations window, you should find a new representation with the residues you have selected using the Sequence